Structural and functional nuclear organization of the beta-globin gene locus in vivo.
Lead Research Organisation:
Babraham Institute
Department Name: Epigenetics
Abstract
The DNA sequence of the human genome has provided a tremendous insight into our genetic make-up. However the DNA sequence alone has provided few clues as to how genetic information is controlled so that the correct genes are activated at the right time during development and in the proper tissues. We have found that gene regulation is extremely complex with multiple levels of control. Cells package inactive genomic regions into compact structures within the nucleus that may play a role in keeping the genes in those regions silent. Active genes on the other hand are relatively decondensed and highly mobile within the confines of a defined nuclear space. We have shown that individual genes communicate with distal genomic sequence that contain important regulatory information by direct physical contact. Futhermore we have shown that active genes often congregate in discrete nuclear locations that seem to be important for their expression. We will investigate the events necessary for the communication between genes and distal regulatory sequences and the congregation or organization of active genes in the nucleus. This information is vital to understand normal gene function as well as what goes wrong in cases were genes are deregulated such as in cancer.
Technical Summary
The proposed experiments will investigate the higher-order structure (chromosome folding) and functional nuclear organization (placement in the nucleus) of genes during transcriptional activity and inactivity. We have found that widely separated genes on the same chromosome often co-localize when they are transcriptionally active, at frequencies much higher than would be expected by random association. Taken together with published reports, which show high chromatin mobility, individual genes adopting distinct nuclear localizations in association with transcriptional activity and nuclear sub-compartments rich in transcriptional apparatus, these data suggest that gene activity is controlled in part by nuclear organization. We have shown that the beta-globin genes and the distal beta-globin locus control region physically associate in vivo during the process of transcription. This higher-order structure appears to be dependent on modifications to the histone tails of chromatin in sub-domains encompassing the developmentally specific genes. These modifications in turn are dependent on intergenic transcription through the subdomain region suggesting that the process of transcription or the presence of the non-coding RNA targets remodelling and histone modification factors to the sub-domains. However another non-exclusive hypothesis is that intergenic transcription itself is involved in the assembly of higher-order structures by acting as a molecular motor to pull distal regions into functional complexes. We will investigate these models and attempt to determine a hierarchy of events that take place in the normal control of gene expression. We will use state-of-the-art techniques such as RNA TRAP, 3C, and 3D confocal RNA and DNA FISH to assess higher-order chromatin structures as well as coordinate nuclear organization of genes as far apart as 40 Mb. In addition we will develop a high-throughput assay to rapidly build up information about the functional organization of the nucleus from numerous genomic perspectives. This information is vital to understanding normal gene function as well as in cases were genes are deregulated as in cancer.
Organisations
- Babraham Institute, United Kingdom (Fellow, Lead Research Organisation)
- Hebrew University of Jerusalem (Collaboration)
- University of Chicago, United States (Collaboration)
- Babraham Institute (Collaboration)
- Friedrich Miescher Inst of Biomed Res (Collaboration)
- Agency for Science, Technology and Research (A*STAR) (Collaboration)
- Medical Research Council (Collaboration)
- University of Michigan, United States (Collaboration)
People |
ORCID iD |
Peter Fraser (Principal Investigator / Fellow) |
Publications

Eskiw CH
(2011)
Ultrastructural study of transcription factories in mouse erythroblasts.
in Journal of cell science

Fraser P
(2007)
Nuclear organization of the genome and the potential for gene regulation.
in Nature

Goren A
(2006)
Fine tuning of globin gene expression by DNA methylation.
in PloS one

Hadjur S
(2009)
Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus.
in Nature


Mitchell JA
(2008)
Transcription factories are nuclear subcompartments that remain in the absence of transcription.
in Genes & development

Nagano T
(2013)
Single-cell Hi-C reveals cell-to-cell variability in chromosome structure.
in Nature

Osborne CS
(2007)
Myc dynamically and preferentially relocates to a transcription factory occupied by Igh.
in PLoS biology

Sexton T
(2007)
Gene regulation through nuclear organization.
in Nature structural & molecular biology

Sexton T
(2007)
The role of transcription factories in large-scale structure and dynamics of interphase chromatin.
in Seminars in cell & developmental biology
Description | BBSRC Project Grant |
Amount | £380,000 (GBP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 03/2007 |
End | 03/2010 |
Description | BBSRC Project Grant |
Amount | £450,000 (GBP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 03/2006 |
End | 03/2009 |
Description | EU FP7 |
Amount | £1,000,000 (GBP) |
Organisation | European Commission |
Department | Seventh Framework Programme (FP7) |
Sector | Public |
Country | European Union (EU) |
Start | 01/2011 |
End | 12/2015 |
Description | MRC Project Grant |
Amount | £380,000 (GBP) |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 11/2008 |
End | 10/2011 |
Title | Array and sequence data |
Description | Genome wide microarray data using e4C and RNA polII ChIPseq data |
Type Of Material | Database/Collection of Data/Biological Samples |
Year Produced | 2009 |
Provided To Others? | Yes |
Impact | publication in press |
Title | Transcription factory model |
Description | Greatly improved understanding of transcriptional organization in mammalian cells |
Type Of Material | Model of mechanisms or symptoms - mammalian in vivo |
Year Produced | 2006 |
Provided To Others? | Yes |
Impact | Advance of the field |
Title | enhanced 4C (e4C) |
Description | Imporoved 4C technique |
Type Of Material | Technology assay or reagent |
Year Produced | 2008 |
Provided To Others? | Yes |
Impact | paper in press |
Description | Cohesin collaboration |
Organisation | Medical Research Council (MRC) |
Department | MRC Clinical Sciences Centre (CSC) |
Country | United Kingdom |
Sector | Public |
PI Contribution | We provided technical expertise and training |
Impact | 19458616 |
Start Year | 2008 |
Description | Goren |
Organisation | Hebrew University of Jerusalem |
Country | Israel |
Sector | Academic/University |
PI Contribution | Contributed transgenic mice and gene expression data |
Impact | 17183675 |
Description | Highthroughput DNA sequencing of e4C and ChIP material |
Organisation | Agency for Science, Technology and Research (A*STAR) |
Department | Genome Institute of Singapore |
Country | Singapore |
Sector | Academic/University |
PI Contribution | We provided material for them to sequence. We then analyzed the results. |
Collaborator Contribution | Performed high throughput DNA sequencing for us. |
Impact | Schoenfelder S, Sexton T, Chakalova L, Cope NF, Horton A, Andrews S, Kurukuti S, Mitchell JA, Umlauf D, Dimitrova DS, Eskiw CH, Luo Y, Wei CL, Ruan Y, Bieker JJ, Fraser P. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet. 2010 Jan;42(1):53-61. |
Start Year | 2006 |
Description | Intergenic paper |
Organisation | University of Chicago |
Country | United States |
Sector | Academic/University |
PI Contribution | We performed the experiments and wrote the paper |
Collaborator Contribution | Provided transgenic mice |
Impact | 17637845 |
Description | Myc paper |
Organisation | Babraham Institute |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We did 95% of the work and wrote the paper |
Collaborator Contribution | Supplied us with DNA probes and expertise. |
Impact | 17622196 |
Description | NSMB Review |
Organisation | Friedrich Miescher Institute for Biomedical Research (FMI) |
Country | Switzerland |
Sector | Academic/University |
PI Contribution | Co-authored review |
Impact | 17984967 |
Start Year | 2006 |
Description | Nature Review |
Organisation | Medical Research Council (MRC) |
Department | MRC Human Genetics Unit |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Co-authored a review |
Impact | 17522674 |
Start Year | 2007 |
Description | Review |
Organisation | University of Michigan |
Country | United States |
Sector | Academic/University |
PI Contribution | Co-authored a review with Doug Engel |
Impact | 16751176 |
Start Year | 2006 |
Description | BBC news website |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Primary Audience | Public/other audiences |
Results and Impact | Interviewed and quoted on BBC News webite none |
Year(s) Of Engagement Activity | 2008 |
Description | BBC radio interview |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Primary Audience | Public/other audiences |
Results and Impact | Radio interview on local radio none |
Year(s) Of Engagement Activity | 2009 |
Description | Judge of Science competition |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Primary Audience | Schools |
Results and Impact | Judge student projects in a one day science competition involving 5 different colleges. none |
Year(s) Of Engagement Activity | 2009 |
Description | Researcher in residence |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | Yes |
Primary Audience | Schools |
Results and Impact | Visit to schools none |
Year(s) Of Engagement Activity | 2007,2008 |
Description | School visit SVC |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Primary Audience | Schools |
Results and Impact | Lectures at local Village College Student spent two weeks in the lab as part of work experience |
Year(s) Of Engagement Activity | 2009,2010 |
Description | Schools day |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | Yes |
Primary Audience | Schools |
Results and Impact | Hosted students for day of experiments none |
Year(s) Of Engagement Activity | 2006,2007,2008,2009,2010 |